REF: group-timepoints/engraftment pipeline take to_baseline param

[cherman2]

This PR refactors group-timepoints action and engraftment pipeline allow "to_baseline" parameter.

This PR changed

• group-timepoints now has distance_to and baseline_timepoint param.
• engraftment pipeline now has distance_to and baseline_timepoint param.
• error handling for mis-matching allowed parameters. users can pass distance_to = donor and a reference column or distance_to = baseline and baseline_timepoint parameter.
• refactored group-timepoints to prepare a dist for to_baseline comparison.

TODO:

• Tests

[lizgehret]

this all generally lgtm @cherman2! all of the comments below are just tiny formatting adjustments (from single quotes to ``) - this will just format those params nicely in the command line.

[cherman2]

Thanks @lizgehret. I definitely agree that `` is more readable. I'll remember to do that next time i'm adding error messages!

[cherman2]

These tests failures are happening when my typeMap for group-column = false. I need to figure out what the other type maps are doing to make this work. I am kinda getting confused between my PRs. I feel like this PR shouldn't have group-column (that should come from #78)

[lizgehret]

These tests failures are happening when my typeMap for group-column = false. I need to figure out what the other type maps are doing to make this work. I am kinda getting confused between my PRs. I feel like this PR shouldn't have group-column (that should come from #78)

Oh weird, I don't see those test failures here, only in #78 (at least in these latest CI runs). I'll reply on that PR re: those particular test failures (the ones in this PR aren't interesting).

[cherman2]

You are right they are only on #78. I need to do a better job of naming concurrence prs . I think I am literally confusing these prs because they both start with REF: group-timepoints.

[lizgehret]

all very small things @cherman2 - once these are updated, i'll pull this down locally to make sure all tests pass and then this should be gtm!

[lizgehret]

Okay @cherman2, this all lgtm - when I replace GroupDist instances (still present on this branch) with Dist1D and run tests locally, they all pass. Would you prefer I wait until #78 is merged to merge this one? Tests won't pass until that PR is merged b/c of the type updates - but realistically it'll be fine either way (since we're going to get that one merged soon too).

[cherman2]

I guess I think just merge it because my CI isn't set-up yet and we will be merging #78 soon. but I definitely defer to your opinion!